An integrated Hutt Valley school may have overcharged parents more than $300,000 in compulsory fees, but the Ministry of Education has no power to make the school admit it.

Hutt International Boys' School (Hibs), which was integrated into the state system in 1994, is required by law to have attendance dues approved by the ministry and published in the Education Gazette before charging them.

The 650-pupil school overcharged parents by nearly 15 per cent, or about $300, in 2010 and 2011 fees, the ministry found.

While the school denies any overcharging or refunds occurred, the parent of a former pupil claims he received overpayment refunds from 2009 and 2010.

Hutt City councillor Max Shierlaw, whose son finished at Hibs at the end of 2010, was told of a "discrepancy" in the fees after he went to the ministry with his concerns.

He was told any refund would have to be sought from the school, and that the ministry had no authority under the Private Schools Conditional Integration Act 1975 to direct or require the school to publicly notify parents of their right to seek a refund.

He received a $742.98 cheque from Hibs board chairman John Ross in August, the exact amount he had been demanding as a refund for overpaid attendance dues.

Mr Shierlaw has openly criticised Hibs in the past, when he accused it of blatant contravention of its Christian "special character" in 2011. He wants the ministry to ensure parents know they may have been overcharged compulsory fees.

"If Hibs won't, then by default, I think it falls back on the Ministry of Education to tell the public about the matter.

"I've been trying to say, I've got my refund, but what about the other parents? That should have been picked up, in my view, in an audit."

No-one knew exactly when the school began overcharging, he said. "Where is the checks and balances here with integrated schools? This may just be the tip of the iceberg."

A ministry spokeswoman said Hibs had overcharged fees since term two in 2010. All parents who paid more than $2362.50 including GST in attendance dues for the last three terms of 2010 and all of 2011 were overcharged.

Although it could not force the school to inform parents of their right to seek a refund, the ministry was communicating with the school about steps it may have taken with parents to rectify the matter.

In a letter to Mr Shierlaw, the ministry said Hibs believed it had been given approval for fees to be increased by $300, and proceeded to charge parents despite having no lawful authority.